Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103173
Name   oriT_pCC1410-2 in_silico
Organism   Klebsiella pneumoniae strain ST709
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY288024 (12540..12625 [-], 86 nt)
oriT length   86 nt
IRs (inverted repeats)      61..68, 73..80  (TTGGTGGT..ACCACCAA)
 27..34, 37..44  (GCAAAAAC..GTTTTTGC)
 8..14, 20..26  (TGATTTA..TAAATCA)
Location of nic site      53..54
Conserved sequence flanking the
  nic site    		  TGTGTGGTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 86 nt

>oriT_pCC1410-2
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   2121 GenBank   WP_000069777
Name   traC_HTK80_RS00160_pCC1410-2 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99195.86 Da        Isoelectric Point: 6.1126

>WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

  Protein structure



No available structure.



ID   2122 GenBank   WP_046072940
Name   traD_HTK80_RS00255_pCC1410-2 insolico UniProt ID   _
Length   753 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 753 a.a.        Molecular weight: 85667.46 Da        Isoelectric Point: 5.1644

>WP_046072940.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPP
GISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 11972..40115

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTK80_RS00045 (PCC1410-2_1_00009) 7944..8378 + 435 WP_000845953 conjugation system SOS inhibitor PsiB -
HTK80_RS00050 (PCC1410-2_1_00010) 8375..9094 + 720 WP_001276217 plasmid SOS inhibition protein A -
HTK80_RS00515 (PCC1410-2_1_00011) 9316..9465 + 150 Protein_11 plasmid maintenance protein Mok -
HTK80_RS00055 (PCC1410-2_1_00011) 9407..9532 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTK80_RS00500 9851..10147 - 297 Protein_13 hypothetical protein -
HTK80_RS00070 (PCC1410-2_1_00012) 10447..10743 + 297 WP_001272251 hypothetical protein -
HTK80_RS00075 (PCC1410-2_1_00013) 10854..11675 + 822 WP_001234445 DUF932 domain-containing protein -
HTK80_RS00080 (PCC1410-2_1_00014) 11972..12574 - 603 WP_000243713 transglycosylase SLT domain-containing protein virB1
HTK80_RS00085 (PCC1410-2_1_00015) 12897..13280 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HTK80_RS00090 (PCC1410-2_1_00016) 13474..14145 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HTK80_RS00095 14282..14509 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HTK80_RS00100 (PCC1410-2_1_00017) 14542..14901 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HTK80_RS00105 (PCC1410-2_1_00018) 14916..15227 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HTK80_RS00110 (PCC1410-2_1_00019) 15249..15815 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HTK80_RS00115 (PCC1410-2_1_00020) 15802..16530 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HTK80_RS00120 (PCC1410-2_1_00021) 16530..17981 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HTK80_RS00125 (PCC1410-2_1_00022) 17971..18537 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HTK80_RS00130 (PCC1410-2_1_00023) 18524..18844 + 321 WP_001057307 conjugal transfer protein TrbD -
HTK80_RS00135 (PCC1410-2_1_00024) 18841..19356 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HTK80_RS00140 19491..19712 + 222 WP_001278683 conjugal transfer protein TraR -
HTK80_RS00145 (PCC1410-2_1_00025) 19705..20181 + 477 WP_000549587 hypothetical protein -
HTK80_RS00150 (PCC1410-2_1_00026) 20261..20479 + 219 WP_000556745 hypothetical protein -
HTK80_RS00155 (PCC1410-2_1_00027) 20507..20854 + 348 WP_000836682 hypothetical protein -
HTK80_RS00160 (PCC1410-2_1_00028) 20980..23610 + 2631 WP_000069777 type IV secretion system protein TraC virb4
HTK80_RS00165 (PCC1410-2_1_00029) 23607..23993 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HTK80_RS00170 (PCC1410-2_1_00030) 23990..24622 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HTK80_RS00175 (PCC1410-2_1_00031) 24619..25611 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTK80_RS00180 (PCC1410-2_1_00032) 25641..25946 + 306 WP_000224416 hypothetical protein -
HTK80_RS00185 (PCC1410-2_1_00033) 25955..26593 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTK80_RS00190 (PCC1410-2_1_00034) 26590..28440 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTK80_RS00195 (PCC1410-2_1_00035) 28467..28724 + 258 WP_000864353 conjugal transfer protein TrbE -
HTK80_RS00200 (PCC1410-2_1_00036) 28711..29460 + 750 WP_001336806 type-F conjugative transfer system pilin assembly protein TraF traF
HTK80_RS00205 (PCC1410-2_1_00037) 29474..29818 + 345 WP_000556796 conjugal transfer protein TrbA -
HTK80_RS00210 (PCC1410-2_1_00038) 29937..30221 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HTK80_RS00215 (PCC1410-2_1_00039) 30208..30753 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTK80_RS00220 30683..31030 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HTK80_RS00225 (PCC1410-2_1_00040) 31011..31403 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HTK80_RS00230 (PCC1410-2_1_00041) 31381..32763 + 1383 WP_001309243 conjugal transfer pilus assembly protein TraH traH
HTK80_RS00235 (PCC1410-2_1_00042) 32760..35582 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HTK80_RS00240 (PCC1410-2_1_00043) 35598..36083 + 486 WP_000605870 hypothetical protein -
HTK80_RS00245 (PCC1410-2_1_00044) 36132..36863 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HTK80_RS00250 (PCC1410-2_1_00045) 37066..37803 + 738 WP_000199905 hypothetical protein -
HTK80_RS00255 (PCC1410-2_1_00046) 37854..40115 + 2262 WP_046072940 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3616 GenBank   NZ_KY288024
Plasmid name   pCC1410-2 Incompatibility group   IncFII
Plasmid size   82841 bp Coordinate of oriT [Strand]   12540..12625 [-]
Host baterium   Klebsiella pneumoniae strain ST709

Cargo genes

Drug resistance gene   blaNDM-5, sul1, qacE, aadA2, dfrA12
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIF11